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TEST: Use existing file to test BET shell task #281

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TEST: Use existing file to test BET shell task #281

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9c16ed9
small fix to the bet exampel
djarecka Jun 16, 2020
4967853
Update pydra/engine/tests/test_shelltask.py
djarecka Jun 16, 2020
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6 changes: 4 additions & 2 deletions pydra/engine/tests/test_shelltask.py
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Original file line number Diff line number Diff line change
Expand Up @@ -2267,12 +2267,14 @@ def change_name(file):
)

# TODO: not sure why this has to be string
in_file = Path(os.path.dirname(os.path.abspath(__file__))) / "data" / "foo.nii"
in_file = (
Path(os.path.dirname(os.path.abspath(__file__))) / "data_tests" / "test.nii.gz"
)
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# separate command into exec + args
shelly = ShellCommandTask(
name="bet_task", executable="bet", in_file=in_file, input_spec=bet_input_spec
)
assert shelly.inputs.executable == "bet"
assert shelly.cmdline == f"bet {in_file} {in_file}_brain"
# res = shelly(plugin="cf")
res = shelly(plugin="cf")
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since we don't really want to run bet in pydra, should we just remove the actual execution?

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we actually don't run this test... see the decorator